C-DEBI Newsletter – March 15, 2016
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Geomicrobiology Journal
Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy
Amy R. Smith*, Martin R. Fisk, Andrew R. Thurber, Gilberto E. Flores, Olivia U. Mason, Radu Popa & Frederick S. Colwell*
*C-DEBI Contribution 320

Volcanic ocean crust contains a global chemosynthetic microbial ecosystem that impacts ocean productivity, seawater chemistry, and geochemical cycling. We examined the mineralogical effect on community structure in the aquifer ecosystem by using a four-year in situ colonization experiment with igneous minerals and glasses in IODP Hole 1301A on the Juan de Fuca Ridge. Microbial community analysis and scanning electron microscopy revealed that olivine phases and iron-bearing minerals bore communities that were distinct from iron-poor phases. Communities were dominated by Archaeoglobaceae, Clostridia, Thermosipho, Desulforudis, and OP1 lineages. Our results suggest that mineralogy determines microbial composition in the subseafloor aquifer ecosystem.

Meetings & Activities

C-DEBI 2015-2016 Networked Speaker Series: Thursday, March 31, 2016, 12pm PT online!

Dr. Katrina Twing, University of Utah
Microbial diversity and metabolic potential of the serpentinite subsurface environment

Serpentinization is the hydrous alteration of mafic rocks to form serpentine minerals and magnetite. The reactions of this alteration result in elevated pH of the surrounding fluids, abiotic generation of H2, CH4(and other organic molecules), and depletion of dissolved inorganic carbon. Thus, serpentinization has implications for the origin of life on Earth and possibly Mars and other planetary bodies with water. The Coast Range Ophiolite Microbial Observatory (CROMO), a set of wells drilled into the actively serpentinizing subsurface environment in northern California, was established in northern California to gain a better understanding of the habitability and microbial functions within the serpentinite subsurface environment. The CROMO wells represent a broad range of geochemical gradients and pH and the concentrations of carbon monoxide and methane have the strongest correlation with microbial community composition. The most extremely high pH wells were inhabited exclusively by a single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia, while more moderate pH wells exhibited greater diversity. Genes involved in the metabolism of hydrogen, carbon monoxide, and carbon fixation were abundant in the extreme pH fluids, while genes for metabolizing methane were exclusively in the moderate pH wells. The subsurface environment is an amalgamation of fluids and rocks, and as such, studying fluids alone only gives half the story. CROMO represents the first drill campaign into the continental serpentinite environment and the microbial diversity of serpentinite cores to a depth of 45 meters below surface suggests that specific geological features harbor different microbial communities. Different core-enriched taxa were correlated with distinct lithostratigraphic zones within the heterogeneous cores, suggesting that mineralogy may impact community composition. These data give us a more comprehensive understanding of the inhabitants of the serpentinite subsurface environment and their geochemical surroundings.

Instructions will be sent via the C-DEBI mailing list on how to listen to the talk and participate in the Q&A online. The Networked Speaker Series is broadcast as an Adobe Connect videoconference run through your internet browser. The presentation will be recorded and available on the website for those unable to “attend” the live web event.

And a hearty congratulations to previous Networked Speaker Series speaker, and C-DEBI Ethics Panel Chair, Karen Lloyd for her recent election to the executive committee of the DCO!

Harvard: Northeastern Geobiology Symposium 2016
The Northeastern Geobiology Symposium is an annual daylong conference organized between the northeastern universities to encourage interaction, strengthen existing ties and build new collaborations in the Geobiology community. In particular, this conference is an excellent opportunity for graduate students to meet collaborators as well as for undergraduate students to meet prospective graduate advisors. The topics of interest will broadly revolve around the themes of environmental geomicrobiology and the co-evolution of life and environment through geological time. Please register confirm your attendance and submit the abstract by TODAY, March 15, 2016.

IODP-USSP: Host An Ocean Discovery Lecture
Are you interested in having an Ocean Discovery Lecturer, such as C-DEBI researchers Andy Fisher and Jason Sylvan, speak at your institution? We accept applications from any U.S. college, university, or nonprofit organization, and the application period is open until May 20, 2016.

SoCal Geobiology Symposium: Call for Abstract Submissions
The 13th annual Southern California Geobiology Symposium will be held on Saturday, May 7th 2016 at the California Institute of Technology (see program for details). Abstract submission deadline: April 01, 2016.


Education & Outreach

C-DEBI: The Community College Research Internship for Scientific Engagement, June 13 - August 5, 2016
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Marine Biological Laboratory in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications due March 18, 2016.

MBL: Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS), August 3 – August 13, 2016
Deep DNA sequencing using massively-parallel, next-generation technology has enabled nearly comprehensive environmental surveys that can describe the different kinds of microbes in a community and their relative abundance. These descriptions of richness and evenness make possible estimates of microbial diversity, but the size of the required data sets pose enormous computational challenges. The rapidly expanding flow of information from next generation DNA sequencing platforms has fueled healthy debate about best practices for data analysis while at the same time building a user demand for tools that can address important ecological questions. The STAMPS course will promote dialogue and the exchange of ideas between experts in analysis of metagenomic data and offer interdisciplinary bioinformatic and statistical training to practitioners of molecular microbial ecology and genomics. The course is designed for established investigators, postdoctoral fellows and advanced graduate students from diverse biological fields. Application deadline: April 8, 2016.

MARUM: ECORD Summer School 2016: Submarine Geohazards - Mapping, Monitoring, and Modelling
Submarine landslides and earthquakes as well as subsequent tsunamis are major geohazards that can pose significant risks to coastal populations and to seafloor infrastructures. Improving our understanding of when, where, and how slope failures and earthquakes occur as well as the assessment of their risk potential are among the most urgent and challenging tasks in Earth sciences. A combination of cutting–edge technologies, including geoscientific mapping, seafloor geodesy, long-term monitoring, sediment coring, and ocean drilling, is needed to gain deeper insights into the interactions among tectonic movements, rock/sediment physical properties, in situ stress, and transient pore pressure. The major goal of the course is to bring PhD students and young Postdocs in touch with IODP at an early stage of their career, inform them about the exciting research within IODP, and to prepare them for future participation in IODP expeditions. Such training will be achieved by taking the summer school participants on a “virtual ship” where they get familiarized with a wide spectrum of state-of-the-art analytical technologies and core description and scanning methods according to the high standards of IODP expeditions. In addition, the thematic topic of the summer school will be reviewed by various scientific lectures by the leading experts in the field. The application deadline is May 05, 2016.

Summer Institutes on Undergraduate STEM Education
The Summer Institutes model the scientific teaching principles they teach. We invite college and university faculty, instructional staff, and future faculty to develop teaching skills at multi-day workshops to transform the undergraduate classroom. They draw on the expertise of participants and presenters. Current research, active learning, assessment, and inclusive teaching are woven into the program, creating a forum to share ideas and develop innovative instructional materials to be implemented upon returning home.

The Data Incubator: Data Science Fellowship
The Data Incubator is a Cornell-funded data science training organization. We run an 8-week fellowship for PhDs looking to enter industry. A variety of innovative companies partner with The Data Incubator for their hiring and training needs, including LinkedIn, Genentech, Capital One, Pfizer, and many others. The program is free for admitted Fellows. Early deadline: March 28, 2016. Regular deadline: April, 04 2016.

IODP-USSSP: ECORD Summer School 2016: Petrophysics
To apply for U.S. travel support, visit the USSSP webpage and scroll down to "Participation" to submit an online application. The deadline to apply for travel support and for the course is April 01, 2016.


Proposal Calls

IODP: Call for Scientific Drilling Proposals
Next proposal submission deadline: April 01, 2016.

DCO/AGI: Diversity Engagement Grants
AGI (American Geosciences Institute) has received funding from the Alfred P. Sloan Foundation to bolster participation of traditionally underrepresented geoscientists within the Deep Carbon Observatory (DCO) community. Please submit all materials by May 02, 2016

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 2016.

DCO: Deep Life Cultivation Internship Program
The DLC will support early-carrier researchers to visit some key laboratories (Inagaki - Kochi, Japan, Bartlett - La Jolla, USA, and others) to learn and practice newly developed cultivation and cultivation-dependent molecular/biogeochemical techniques using samples from the DLC’s field missions. Financial support includes $5,400 per person for travel and lodging costs and host lab research supply reimbursement. Interested applicants should send their cv, a brief one page statement of their cultivation plans, and a letter of support from their intended host to Fumio Inagaki ( and Douglas Bartlett (

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops, related to the International Ocean Discovery Program (IODP).


IODP at Texas A&M: Assistant Research Scientist
The International Ocean Discovery Program (IODP) at Texas A&M University invites applications for an Assistant Research Scientist (Expedition Project Manager/Staff Scientist) in our Science Operations section. Preference will be given to applicants with expertise in petrology, inorganic (fluid) geochemistry, downhole logging, petrophysics, and sedimentology. However, applicants in any field of geoscience pertinent to IODP will be considered. A Ph.D. in geosciences or related field, and demonstrated on-going research experience is required. Experience as a seagoing scientist, especially in scientific ocean drilling, is preferred. This position will serve as the Expedition Project Manager to coordinate all aspects of precruise expedition planning, sea-going implementation, and postcruise activities. These duties include sailing as the IODP scientific representative on a two-month IODP expedition approximately once every 1 to 2 years. Individual scientific research, as well as collaboration with colleagues at Texas A&M University in fulfilling its educational mission, is required. This position will also provide scientific advice on laboratory developments in their area of specialization including scientific implementation of downhole logging on the JOIDES Resolution. We will begin reviewing applications on May 16, 2016, but will continue to accept applications until candidates are selected for interviews.

Bigelow: Research Technician
The Deep Biosphere laboratory at the Bigelow Laboratory for Ocean Sciences ( is seeking a qualified and highly motivated individual for a full-time or part-time Research Technician position. Highly successful candidates would have experience with environmental science and/or microbiology, with working knowledge of molecular biology techniques (such as DNA extraction, amplification, sequencing, bioinformatics) and/or microscopy considered as highly desirable. Experience with project management also desired. Proficiency in computer programs for word processing and data entry and good communication skills a must. Applicant must have at minimum a B.S. degree. Research will be conducted primarily at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, but opportunities may be available for fieldwork. The position is initially offered for one year with continuation for additional years based upon successful job performance. The position is available immediately, but this may be negotiated. Salary will be commensurate with prior experience. Review of applicants will begin on April 11, 2016.

Cardiff University: Senior Lecturer / Reader / Chair in Geomicrobiology, School of Earth and Ocean Sciences
Closing date: March 31, 2016.

IFREMER: Life at the extremes: microbial EcoGenomics of deep-sea extremophiles: Postdoctoral position (starting immediately) 
The Lab for Microbiology of Extreme environments in Brest (France) has an 18-month postdoctoral position available to carry out research in the ecology of bacterial and archaeal communities in deep-sea brine lakes and hydrothermal vent systems. The appointment should start no later than April 1 2016. Please send inquiries and application to Loïs Maignien ( and A.M. Eren (


Don’t forget to email me with any items you'd like to share in future newsletters! You are what makes our deep biosphere community!
Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

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